Not sure if this will help but I had some alternator/engine noise when I installed some component sets a few months ago. Had them running off a rf 400a4 and when on low volume, pause, or when I gave it gas you could really hear the noise.

The solution for me was a Filter box. Local shop here hooked me up with it and charged me $18. It hooks up to the power wires coming from the battery and then goes on to the amp. I never seen anything like it before but it works well. No more noise.

40GB Blue mkII